Emerging infectious diseases and pandemics in humans often originate from pathogens transmitted from nonhuman animal reservoirs. The pandemics of severe acute respiratory syndrome, HIV, and 2009 H1N1 influenza illustrate the dramatic impact of viral host-switching on public health and the global economy. Early prediction, detection, characterization, and risk assessment of viruses in their animal hosts, before they spread into the human population, are critical to protect public health.
Most influenza A viruses circulate in waterfowl, but those that infect mammalian hosts are thought to pose the greatest risk for zoonotic spread to humans and the generation of pandemic or panzootic viruses. Bats (order Chiroptera) are of particular interest, because they comprise nearly 1,200 species worldwide, accounting for approximately one-fourth of all mammalian species, and their global distribution, abundance, ability to fly and migrate over large distances, and sociality favors the acquisition and spread of viruses. In recent history, bats have been sources of multiple pathogenic viruses for humans and domestic animals, including coronaviruses, filoviruses, henipaviruses, and lyssaviruses. Pathogen-specific assays which are commonly used in the laboratory however, are not always sufficient to determine the etiology of cases or outbreaks of viral disease. Thus, there is a need to detect previously known as well as novel influenza viruses and influenza-related viruses in human and animal populations.